Posts from the ‘omics’ Category

Big Week for “Synthetic” Biology

A jellyfish made of silicone, and a bacterium made in silico

Synthetic biology is traditionally thought of as repurposing existing or designing new biological parts to do novel things. But in a larger sense, it can be thought of as the ability to create biological systems outside the limitations of pesky things like global and evolutionary time scales. This week marks two really stunning bio accomplishments, each fitting into their own definition of “synthetic”.

Whoa, Jellyman: Cal Tech and Harvard biophysicists announced that they had created a sort of “synthetic jellyfish” this week (pictured above left). By taking thin, carefully designed sheets of silicone and layering rat heart muscle cells over them, they were able to make a bell-shaped living device that pulsed and swam just like the bell of a jellyfish.

Heart muscle cells, or cardiomyocytes, naturally grow together in sheets and will automatically “beat” in a petri dish (with the help of a little calcium). If you provide an outside voltage (like a pacemaker) they will beat in unison! The rat-heart-silicone “medusoid” shape contracted, with the beating cells pulling on the silicone substrate just as a jellyfish’s own muscle cells act on its bell to swim.

They modeled, on a very general scale, the tiny bacterium Mycoplasma genitalium, which only has 525 genes compared to our ~20,000, and all of its internal processes on 128 computers operating for 10 hours. To complete a single cell division, it required half a gigabyte of data. But you have to be careful before you call this a completely “simulated organism”. Normal cells have many, perhaps hundreds, of just different types of genes, and they interact in myriad ways … we have just begun to scratch the surface of those networks. Just look at how complicated even the tiny changes in a cancer cell can be!

By simplifying their model down to 28 minimal systems, their computer program matched the bacterium’s biology as we know it. But a more “realistic” model is going to be exponentially more complicated. Here’s some collected reactions at Tree of Life. But, still … wow!

Modern biology has done a very good job at describing the function of individual genes and proteins, but our next chapter lies in how these interactions build into systems. The “-omics” era will be one where we map how the thousands of parts that we are made of combine to make us whole.Simulations like this will be at the leading edge of that era. But we have a long way to go … how many computers would it take to model the trillions of cells in the human body?